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Posts Tagged ‘ Phylogenetics ’

Yesterday my paper appeared in early view in Evolution (author’s preprint),1 so I’d like to take this chance to share the back-story and highlight my own view on some of our findings, and the associated package on CRAN.2 I didn’t set out to write this paper. I set out to write a very different

My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition … Continue reading →

My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition requirements at journals such as Evolution, Am Nat, and Sys Bio, and data management plan

There is an awesome position opening up for an assistant professor in systematics at the University of Vermont. Below is the announcement, and see the original post at the Distributed Ecology blog. Why is this related to R? One can do a lot of systemat...

While high-speed fish feeding videos may be the signature of the lab, dig a bit deeper and you’ll find a wealth of comparative phylogenetic methods sneaking in. It’s a natural union — expert functional morphology is the key to good comparative methods, just as phylogenies hold the key to untangling the evolutionary origins of that

We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn't go this year or last year, definitely think about going next year.Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out):Vistrails...

I am writing a set of functions to search ITIS for taxonomic information (more databases to come) and functions to fetch plant phylogenetic trees from Phylomatic. Code at github.Also, see the examples in the demos folder on the Github site above.

I wrote a simple function for plotting a phylogeny in ggplot2. However, it only handles a 3 species tree right now, as I haven't figured out how to generalize the approach to N species.Any ideas on how to improve this?

My TreeBASE R package is essentially functional now. Here’s a quick tutorial on the kinds of things it can do. Grab the treebase package here, install and load the library into R. TreeBASE provides two APIs to query the database, one which searches by the metadata associated with different publications (called OAI-PMH), and another which